Insights into the ribosome function from the structures of non-arrested ribosome nascent chain complexes

ABSTRACT During protein synthesis, the growing polypeptide chain threads through the nascent peptide exit tunnel that spans the body of the large ribosomal subunit while simultaneously acting as a modulator of ribosomal activity by itself or by sensing various small molecules, such as metabolites or antibiotics appearing in the tunnel. While arrested ribosome nascent chain complexes (RNCCs) have been extensively studied structurally, little attention has been given to the RNCCs that represent the functionally active state of the ribosome. This is in part due to the lack of a simple and reliable procedure for the large-scale preparation of peptidyl-tRNAs. Here we report a new chemoenzymatic approach based on native chemical ligation reaction for the facile synthesis of stably linked peptidyl-tRNAs that were used to determine several structures of RNCCs in the functional pre-attack state of the peptidyl transferase center (PTC) at the highest resolution available to date. These structures reveal a previously unknown role of the ribosome in stabilization of the growing polypeptide within the PTC and suggest an extended entropic trap model that mechanistically rationalizes how ribosome acts with comparable efficiencies upon a multitude of possible growing peptides having various sequences. Our structures also provide new insights into the mechanism of PTC functioning and explain what makes ribosome a versatile catalyst.